GenScale -- v0

1. Setup GenScale by following instructions in SETUP.md.
2. NodeJS backend of GenScale runs on port 3333 of the host node. Suppose node name is 'genscale-node'. We can do port-forwarding to a local machine:

ssh -f -N -L localhost:3333:localhost:3333 genscale-node

Open a browser on the local machine and type 'localhost:3333'.

Deliverables

We provide the following deliverables:

• Source code of GenScale
• How to setup
• Dataset
• Container Images
• Sample Performance Data

1. Source Code

This repository contains all the code needed for setting up GenScale: Link

2. How to Setup

Please check the following file: Link

3. Dataset

As mentioned in SETUP.md, we provide two mirrors for sample dataset, i.e. Chameleon Object Store and Google Drive.

The Goole Drive folder is publicly available here: Link

4. Container Images

The sample DNA-Seq and RNA-Seq workflows requires 7 containers in total. Some of the containers are used in both workflows. We provide both the container images (can be used right away with docker pull) and the source code for building each container.

All containers are merely a repackaging of publicly available tools / applications to suit GenScale's need (e.g. modifying entrypoints). We do not claim ownership of these tools, and we extend heartfelt thanks to the original developers.

Application	Container	Source Code
BWA	Package	Repo
FastQC	Package	Repo
Fastq Cleaner	Package	Repo
GATK	Package	Repo
Picard	Package	Repo
STAR	Package	Repo
Trimmomatic	Package	Repo

5. Sample Performance Data

Data can be found in folder metrics/. An example notebook analyzing the CPU utilization can be found here: Link